Distributed Approach for Peptide Identification

84 Pages·2016·2.31 MB·English

Western Kentucky University
TopSCHOLAR®
Masters Theses & Specialist Projects Graduate School
Fall 2015
Distributed Approach for Peptide Identification
Naga V K Abhinav Vedanbhatla
Western Kentucky University, [email protected]
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Recommended Citation
Vedanbhatla, Naga V K Abhinav, "Distributed Approach for Peptide Identification" (2015).Masters Theses & Specialist Projects.Paper
1546.
http://digitalcommons.wku.edu/theses/1546
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DISTRIBUTEDAPPROACHFORPEPTIDEIDENTIFICATION
AThesis
Presentedto
TheFacultyoftheDepartmentofComputerScience
WesternKentuckyUniversity
BowlingGreen,Kentucky
InPartialFulfillment
OftheRequirementsfortheDegree
MasterofScience
By
NagaVenkataKrishnaAbhinavVedanbhatla
December2015

DEDICATION
Thisthesisisgratefullydedicatedtomyparentsandallmyfriendswhobelievedinme.
ACKNOWLEDGMENTS
I would like to extend my sincere gratitude to my committee chair, Dr. Zhonghang
Xiaforprovidingmethisopportunity. Withouthisguidanceandpersistenthelp,thisthesis
wouldnothavebeenpossible. Ithasbeenagreatpleasuretoworkalongsidehimbothasa
graduateassistantandasastudent.
I would also like to acknowledge Dr. Rong Yang. I am very thankful for the way
that she inspired and motivated me. I appreciate Dr. Yang taking the time to review this
document. ourdiscussionsandherperspectivewascrucialincompletingthisresearch.
I would like to thank Dr. Qi Li who accepted my request to be part of my thesis
committee. Iamextremelygratefulforhisassistanceandsuggestionsthroughtmyresearch
and the coursework. I would also like to extend my sincere gratitude to Western Kentucky
Universityforprovidingmeafriendlyenvironmenttopursuemymastersdegree.
I would also like to thank my friends Travis Brummett and Harinivesh Donepudi
for helping me in revising this document. I would like to extend my appreciation to my
friends Sai Sandeep Jagarlamudi and Kavya Madugula for supporting me during my hard
times.
Finally, I would like to extend my gratitude to my parents who has continuously
supportedmeandbelievedinmeeachandeverymomentofmylife.
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CONTENTS
DEDICATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii
ACKNOWLEDGMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iv
LISTOFTABLES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
LISTOFFIGURES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
ABSTRACT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 ProteinsandPeptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 PeptideandProteinIdentification . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 C-Ranker,PeptideIdentificationandTime . . . . . . . . . . . . . . . . . . 5
1.4 ResearchObjectivesandMethodology . . . . . . . . . . . . . . . . . . . . 7
1.5 Objectivesandplanofthesis . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.6 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.7 Advantages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.8 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2 BACKGROUND . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.1 MassSpectrometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2.2 TandemMassSpectrometry . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.3 PostDatabaseSearchMethods . . . . . . . . . . . . . . . . . . . . . . . . 12
2.3.1 PeptideProphet . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
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2.3.2 Percolator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.3.3 C-Ranker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
2.4 DistributedSystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.4.1 CentralizedsystemVsDistributedSystem . . . . . . . . . . . . . . 18
2.5 WhynotdistributedframeworkslikeHadoop? . . . . . . . . . . . . . . . . 19
2.6 DistributedframeworkeffectsonC-Ranker . . . . . . . . . . . . . . . . . 19
2.7 JavaforDistributedSystems . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.8 DistributedSystemsinnetworkingpoint-of-view . . . . . . . . . . . . . . 21
3 ENVIRONMENTSETUPANDDESIGN . . . . . . . . . . . . . . . . . . . . . 23
3.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.2 JavaRuntimeEnviroment . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3.2.1 InstallingJavaRuntimeEnvironment . . . . . . . . . . . . . . . . 24
3.3 Architecture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3.4 DataFlow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
3.4.1 DataFlowforSingleC-Ranker . . . . . . . . . . . . . . . . . . . 27
3.4.2 DataFlowforDistributedC-Ranker . . . . . . . . . . . . . . . . . 28
4 INFRASTRUCTURESETUPANDEXECUTION . . . . . . . . . . . . . . . . 32
4.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
4.2 InfrastructureSetup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
4.3 ExecutingC-Ranker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
5 RESULTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
5.1 AnalysisofResults . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
vi
5.1.1 MemoryUsage . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
5.2 ComparisonwithC-RankerinanApacheHadoopFramework . . . . . . . 47
6 CONCLUSIONANDFUTUREWORK . . . . . . . . . . . . . . . . . . . . . . 51
REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
APPENDICES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
A SOURCECODECOMMENTARY . . . . . . . . . . . . . . . . . . . . . . . . . 58
A.A ThecalcExcelMethod . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
A.B ExcelDividerdriver . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
A.C ThemergeMethod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
A.D TheserveMethod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
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LISTOFTABLES
5.1 InputDataSetsforObservations . . . . . . . . . . . . . . . . . . . . . . . 40
5.2 HardwareUsedtoObserveResults . . . . . . . . . . . . . . . . . . . . . . 41
5.3 Comparison of C-Ranker on distributed approach with C-Ranker on an
ApacheHadoopFrameworkCluster1 . . . . . . . . . . . . . . . . . . . . . 49
5.4 Upgradedhardwaretocomparewithcluster2Hadoop . . . . . . . . . . . . 49
5.5 Comparison of C-Ranker on distributed approach with C-Ranker on an
ApacheHadoopFrameworkCluster2 . . . . . . . . . . . . . . . . . . . . 49
5.6 CostCalculationofApacheHadoopCluster1andCluster2 . . . . . . . . 50
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LISTOFFIGURES
2.1 DistributedSystem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.2 LANDesign . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.3 Peer-to-PeerNetwork . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.1 InstallingJavaCompilerRuntime(InitialScreen) . . . . . . . . . . . . . . 24
3.2 InstallingJavaCompilerRuntime(LicenseandUserAgreement) . . . . . . 25
3.3 InstallingJavaCompilerRuntime(ConfirmInstallationSettings) . . . . . . 25
3.4 Architecture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3.5 DataFlowDetailsintheOriginalSingle-ThreadedC-Ranker . . . . . . . . 28
3.6 DataFlowDetailsinDistributedC-Ranker(Dividing) . . . . . . . . . . . . 29
3.7 DataFlowForaSingleWorkerHost . . . . . . . . . . . . . . . . . . . . . 30
3.8 DataFlowDetailsinDistributedC-Ranker(Merging) . . . . . . . . . . . . 31
4.1 DownloadApacheTomcat . . . . . . . . . . . . . . . . . . . . . . . . . . 33
4.2 ApacheTomcatExtractedinC:Drive . . . . . . . . . . . . . . . . . . . . 34
4.3 ApacheTomcatServer|startup.bat| . . . . . . . . . . . . . . . . . . . . . . 34
4.4 ApacheTomcatServerRunning . . . . . . . . . . . . . . . . . . . . . . . 35
4.5 ROOT.warfileintheApacheTomcatDirectory . . . . . . . . . . . . . . . 36
4.6 ServerRunner.jarFileMovedtoHomeDirectory . . . . . . . . . . . . . . 36
4.7 CrankerPropertiesFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
4.8 ServerRunner.jarRunningandAskingforAPortNumber . . . . . . . . . . 38
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